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Title :   CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF RECD2 WITH DNA AND ADPNP

Authors :   K. Saikrishnan, N. Cook, D. B. Wigley

Date :   23 Mar 09 (Deposition) - 16 Jun 09 (Release) - 16 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,X,Y
Biol. Unit 1: A,X  (1x)
Biol. Unit 2: B,Y  (1x)

Keywords :   Alpha And Beta Protein, Atp-Binding, Nucleotide-Binding, Helicase, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Saikrishnan, B. Powell, N. J. Cook, M. R. Webb, D. B. Wigley
Mechanistic Basis Of 5'-3' Translocation In Sf1B Helicases.
Cell(Cambridge, Mass. ) V. 137 849 2009
PubMed-ID: 19490894 | Reference-DOI: 10.1016/J.CELL.2009.03.036
(for further references see the PDB file header)

Molecule 1 - EXODEOXYRIBONUCLEASE V, SUBUNIT RECD, PUTATIVE
	Atcc	:	13939
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 151-715
	Gene	:	DR_1902, RECD2
	Organism Scientific	:	DEINOCOCCUS RADIODURANS R1
	Organism Taxid	:	243230
	Other Details	:	N-TERMINUS DELETION MUTANT OF RECD2
	Strain	:	R1 / DSM 20539 / IFO 15346 / LMG 4051 / NCIB 9279

*Molecule 2 - 5'-D(TTPTPTPTPTPTPT)-3'*
	Chains	:	X, Y
	Engineered	:	YES
	Other Details	:	SINGLE-STRANDED OLIGO-DT
	Other Details - Source	:	SYNTHETIC DNA
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	X	Y
Biological Unit 1 (1x)	:	A		X
Biological Unit 2 (1x)	:		B		Y

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	ANP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:136 , SER A:367 , HOH A:739 , HOH A:740 , ANP A:801	BINDING SITE FOR RESIDUE MG A 800
2	AC2	SOFTWARE	HOH A:11 , HOH A:12 , HOH A:136 , GLY A:338 , GLN A:343 , GLY A:361 , PRO A:362 , GLY A:363 , THR A:364 , GLY A:365 , LYS A:366 , SER A:367 , THR A:368 , GLN A:466 , TYR A:492 , ARG A:493 , GLU A:652 , ARG A:679 , HOH A:739 , HOH A:740 , HOH A:742 , MG A:800	BINDING SITE FOR RESIDUE ANP A 801
3	AC3	SOFTWARE	HOH B:88 , SER B:367 , HOH B:725 , HOH B:726 , ANP B:801	BINDING SITE FOR RESIDUE MG B 800
4	AC4	SOFTWARE	HOH B:88 , GLY B:338 , GLN B:343 , PRO B:362 , GLY B:363 , THR B:364 , GLY B:365 , LYS B:366 , SER B:367 , THR B:368 , GLN B:466 , TYR B:492 , ARG B:493 , GLU B:652 , ARG B:679 , HOH B:725 , MG B:800	BINDING SITE FOR RESIDUE ANP B 801

(no "SS Bond" information available for 3GPL)

(no "Cis Peptide Bond" information available for 3GPL)

(no "SAP(SNP)/Variant" information available for 3GPL)

(no "PROSITE Motif" information available for 3GPL)

(no "Exon" information available for 3GPL)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:516
 aligned with RECDL_DEIRA | Q9RT63 from UniProtKB/Swiss-Prot  Length:715

    Alignment length:531
                                   193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713 
          RECDL_DEIRA   184 ALDRLEKDLFTLTEVEGIGFLTADKLWQARGGALDDPRRLTAAAVYALQLAGTQAGHSFLPRSRAEKGVVHYTRVTPGQARLAVETAVELGRLSEDDSPLFAAEAAATGEGRIYLPHVLRAEKKLASLIRTLLATPPADGAGNDDWAVPKKARKGLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTTKAVADLAESLGLEVGLCAPTGKAARRLGEVTGRTASTVHRLLGYGPQGFRHNHLEPAPYDLLIVDEVSMMGDALMLSLLAAVPPGARVLLVGDTDQLPPVDAGLPLLALAQAAPTIKLTQVYRQAAKNPIIQAAHGLLHGEAPAWGDKRLNLTEIEPDGGARRVALMVRELGGPGAVQVLTPMRKGPLGMDHLNYHLQALFNPGEGGVRIAEGEARPGDTVVQTKNDYNNEIFNGTLGMVLKAEGARLTVDFDGNVVELTGAELFNLQLGYALTVHRAQGSEWGTVLGVLHEAHMPMLSRNLVYTALTRARDRFFSAGSASAWQIAAARQREARNTALLERIRA 714
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh..........hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh....eehhhhhhhhhhh.....hhhhhhhhhhhhh...ee.-------------..eeehhhhhhhhhhhhhhhhhhhhh....--.......hhhhhh..hhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhh...eehhhhh.ee..ee...........eeee.hhhhhhhhhhhhhhhh.....eeeee............hhhhhhhhhh.eee..........hhhhhhhhhhh...........eeeee....hhhhhhhhhhhh.......eeee.......hhhhhhhhhhhhhh.....ee....ee....eeee.............eeeeeeee..eeeeee..eeeeehhhhhh.eee..eeehhhhh...eeeeeeeehhhhhhhhhhhhhhhhhh.eeeeeeeeehhhhhhhhhhh.......hhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gpl A 184 ALDRLEKDLFTLTEVEGIGFLTADKLWQARGGALDDPRRLTAAAVYALQLAGTQAGHSFLPRSRAEKGVVHYTRVTPGQARLAVETAVELGRLSED-------------EGRIYLPHVLRAEKKLASLIRTLLATPPAD--GNDDWAVPKKARKGLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTTKAVADLAESLGLEVGLCAPTGKAARRLGEVTGRTASTVHRLLGYGPQGFRHNHLEPAPYDLLIVDEVSMMGDALMLSLLAAVPPGARVLLVGDTDQLPPVDAGLPLLALAQAAPTIKLTQVYRQAAKNPIIQAAHGLLHGEAPAWGDKRLNLTEIEPDGGARRVALMVRELGGPGAVQVLTPMRKGPLGMDHLNYHLQALFNPGEGGVRIAEGEARPGDTVVQTKNDYNNEIFNGTLGMVLKAEGARLTVDFDGNVVELTGAELFNLQLGYALTVHRAQGSEWGTVLGVLHEAHMPMLSRNLVYTALTRARDRFFSAGSASAWQIAAARQREARNTALLERIRA 714
                                   193       203       213       223       233       243       253       263       273     |   -       293       303       313        |- |     333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713 
                                                                                                                         279           293                          322  |                                                                                                                                                                                                                                                                                                                                                                                                     
                                                                                                                                                                       325

Chain B from PDB  Type:PROTEIN  Length:516
 aligned with RECDL_DEIRA | Q9RT63 from UniProtKB/Swiss-Prot  Length:715

    Alignment length:531
                                   193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713 
          RECDL_DEIRA   184 ALDRLEKDLFTLTEVEGIGFLTADKLWQARGGALDDPRRLTAAAVYALQLAGTQAGHSFLPRSRAEKGVVHYTRVTPGQARLAVETAVELGRLSEDDSPLFAAEAAATGEGRIYLPHVLRAEKKLASLIRTLLATPPADGAGNDDWAVPKKARKGLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTTKAVADLAESLGLEVGLCAPTGKAARRLGEVTGRTASTVHRLLGYGPQGFRHNHLEPAPYDLLIVDEVSMMGDALMLSLLAAVPPGARVLLVGDTDQLPPVDAGLPLLALAQAAPTIKLTQVYRQAAKNPIIQAAHGLLHGEAPAWGDKRLNLTEIEPDGGARRVALMVRELGGPGAVQVLTPMRKGPLGMDHLNYHLQALFNPGEGGVRIAEGEARPGDTVVQTKNDYNNEIFNGTLGMVLKAEGARLTVDFDGNVVELTGAELFNLQLGYALTVHRAQGSEWGTVLGVLHEAHMPMLSRNLVYTALTRARDRFFSAGSASAWQIAAARQREARNTALLERIRA 714
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh..........hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh....eehhhhhhhhhhh.....hhhhhhhhhhhhh...ee.-------------..eeehhhhhhhhhhhhhhhhhhhhh....--.......hhhhhh..hhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhh...eehhhhh.ee..ee...........eeee.hhhhhhhhhhhhhhhh.....eeeee............hhhhhhhhhh.eee..........hhhhhhhhhhh...........eeeee....hhhhhhhhhhhh.......eeee.......hhhhhhhhhhhhhh.....ee....ee....eeee.............eeeeeeee..eeeeee..eeeeehhhhhh.eee..eeehhhhh...eeeeeeeehhhhhhhhhhhhhhhhhh.eeeeeeeeehhhhhhhhhhh.......hhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gpl B 184 ALDRLEKDLFTLTEVEGIGFLTADKLWQARGGALDDPRRLTAAAVYALQLAGTQAGHSFLPRSRAEKGVVHYTRVTPGQARLAVETAVELGRLSED-------------EGRIYLPHVLRAEKKLASLIRTLLATPPAD--GNDDWAVPKKARKGLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTTKAVADLAESLGLEVGLCAPTGKAARRLGEVTGRTASTVHRLLGYGPQGFRHNHLEPAPYDLLIVDEVSMMGDALMLSLLAAVPPGARVLLVGDTDQLPPVDAGLPLLALAQAAPTIKLTQVYRQAAKNPIIQAAHGLLHGEAPAWGDKRLNLTEIEPDGGARRVALMVRELGGPGAVQVLTPMRKGPLGMDHLNYHLQALFNPGEGGVRIAEGEARPGDTVVQTKNDYNNEIFNGTLGMVLKAEGARLTVDFDGNVVELTGAELFNLQLGYALTVHRAQGSEWGTVLGVLHEAHMPMLSRNLVYTALTRARDRFFSAGSASAWQIAAARQREARNTALLERIRA 714
                                   193       203       213       223       233       243       253       263       273     |   -       293       303       313        |- |     333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713 
                                                                                                                         279           293                          322  |                                                                                                                                                                                                                                                                                                                                                                                                     
                                                                                                                                                                       325

Chain X from PDB  Type:DNA  Length:7
                                       
                 3gpl X   2 TTTTTTT   8

Chain Y from PDB  Type:DNA  Length:7
                                       
                 3gpl Y   2 TTTTTTT   8

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 3GPL)

(no "CATH Domain" information available for 3GPL)

(no "Pfam Domain" information available for 3GPL)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RECDL_DEIRA | Q9RT63)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0043141	ATP-dependent 5'-3' DNA helicase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; drives the unwinding of the DNA helix in the direction 5' to 3'.
	GO:0004003	ATP-dependent DNA helicase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of the DNA helix.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0008094	DNA-dependent ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of single- or double-stranded DNA, and it drives another reaction.
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0032508	DNA duplex unwinding	The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.

Asymmetric Unit
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(no "Cis Peptide Bonds" information available for 3gpl)

Biological Units
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	RECDL_DEIRA \| Q9RT63	:	3e1s 3gp8

3e1s	CRYSTAL STRUCTURE OF AN N-TERMINAL TRUNCATION OF DEINOCOCCUS RADIODURANS RECD2 (NATIVE STRUCTURE)
3gp8	CRYSTAL STRUCTURE OF THE BINARY COMPLEX OF RECD2 WITH DNA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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